From: Giacomo Fiorin (
Date: Wed Oct 13 2021 - 08:31:26 CDT

Hi, You know more about the operating system you're using than the people
on the mailing list (which is nothing, because you didn't specify it).

Try running namd2 from a command-line prompt or terminal (all OSs have
one), and make sure that you can launch it from there: it should tell you
that a configuration file is missing when you launch it without any
arguments. That same executable should then also work when you launch it
from the plugin.


On Wed, Oct 13, 2021 at 8:02 AM José Villalaín <> wrote:

> Dear all,
> Sorry to ask this question, maybe it shouldn't be done here but I haven't
> found an answer anywhere else.
> I am trying to use the CAFE plugin to obtain binding affinity for a
> trajectory (using a tcl script in VMD). However, it stops at the middle of
> it stating that "couldn´t execute namd2: permission denied" ... I have
> changed ownership of every one of the files and directories and I am stuck
> here not knowing what to do.
> If anyone has any suggestions, I would be very grateful.
> José